Re: [h5md-user] Additional properties of particles

[Felix Höfling]

Hi Jakub,

Am 06.11.2014, 16:11 Uhr, schrieb Jakub Krajniak  
<address@hidden>:

> Hi,
>
> Recently I started to use H5MD (thanks to Pierre de Buyl) but I would  
> like to propose additional properties that seems to be missing.
> 1. The particle charge 'q'. It should behave like the 'mass' property  
> and could be both time-dependent and time-independent.
Good suggestion, we should have included the charge already in 1.0, but  
overlooked them as nobody of us was using electrostatic interactions. The  
charge is clearly a per-particle property just as mass is. The physical  
unit of charge is already covered by the "units" module.

To make things concrete, please open an H5MD proposal for including the  
charge:
http://nongnu.org/h5md/proposals/

> 2. The 'resnr' that will behave like current 'species'. That property  
> should group the particles in molecules. The .gro and .pdb file format  
> have something similar. The residue name is not so important as it could  
> be solved outside the h5md.
This point is less clear. The residual number does not affect the physical  
properties/interactions of the particles (unlike "species" does), its  
primary purpose is for analysis. (Please correct me if I'm mistaken.)

I'm not an expert in proteins, but the residuals seem to describe the  
protein structure on a more coarse-grained level. So it has more  
similarities with topology/connectivity (although it is less stringent).  
What comes to mind is to store information about the residual groups  
outside of the particles tree.

Suggestions: store a list of particle indices (better: IDs) for each  
residual. This makes it easy to look up all particles of given residual,  
however the inverse would be inefficient.

H5MD root
 \-- residuals
      \-- (name)
          \-- particle_subgroup1
          \-- particle_subgroup2

"particle_subgroupX"  are H5MD elements, their names match the  
corresponding subgroups in particle/ and the contents is a list of IDs (or  
just the array index if "id" is not present).

To proceed more efficiently with the discussion, please open an H5MD  
proposal as well.
Thanks for contributing!

Best regards,

Felix